This throws a huge wrench into all of that by signaling to the states that everything could change later regarding mail-in voting.

At the very least, it certainly makes mail in voting much more risky and therefore discourages people from voting that way. I get how the SCOTUS majority can willfully ignore this, but how can smart people like Al and Peter not see this?

I think part of it is people misunderstanding what an Executive Order is.

It's not a law. It's not a regulation. It's the President giving instructions to federal employees. It doesn't bind anyone outside the government.

For Executive Orders that are basically instructions to cabinet levels to do things like draft a regulation, there's no material difference between an EO and the President giving a speech saying, "I am hereby asking the Secretary of Whatever to prepare a regulation that will do X." Or even just telling the Secretary of Whatever to put together that regulation just at a cabinet meeting, or over lunch. If the regulation is unconstitutional, there are opportunities for affected parties to challenge the regulation, and get an injunction against the regulation. But the President saying that he wants his Department head to draft a regulation? No one has their legal rights or interests affected at that time by that act.

If the President gives a speech saying that he wants all these things to happen, it can certainly discourage people from doing certain things - but you can't enjoin him from giving a speech and announcing what he wants his Administration to do in the future. It's just not ripe yet. So it's not really all that surprising that the SCOTUS might lean towards thinking the government's going to prevail on ripeness at this stage.